This paper describes the results of a systematic experimental investigation of the influence of different size alkyl ammonium cations and heteroanions on the composition, ionic charge state and gas-phase fragmentation pathways of anionic polyoxovanadates synthesized in solution. Four separate solutions of polyoxometalates (POMs) were prepared using all possible combinations of the tetraethylammonium [(C2H5)4N+] cation, chloride (Cl−) heteroanion, tetrabutylammonium [(C4H9)4N+] cation and acetate (CH3CO2−) heteroanion. Employing electrospray ionization combined with high-resolution mass spectrometry (ESI-MS) we demonstrate that POM solutions synthesized using the small [(C2H5)4N+] cation and Cl− heteroanion are composed predominately of large doubly and triply charged chlorine containing species with a size distribution centered at 14 vanadium atoms. POM solutions prepared using the Cl− anion and a larger [(C4H9)4N+] cation are shown to contain slightly larger species with 15 and 16 vanadium atoms, thereby indicating that the size of the ammonium cation exerts only a weak influence on the size of polyoxovanadates formed in solution. POM solutions prepared using (C2H5)4NCl and (C4H9)4NCl also produced peaks consistent with the attachment of one and two ammonium cations to the larger vanadium oxide species. Solutions prepared using the large CH3CO2− heteroanion, in contrast, contain much smaller singly and doubly charged species with a size distribution centered at six vanadium atoms. In addition, while incorporation of one and two ammonium cations into the smaller vanadium oxide species was observed, no POMs containing the CH3CO2− heteroanion were identified. The gas-phase fragmentation pathways of representative POMs containing one and two ammonium cations were examined using collision induced dissociation (CID) and mass spectrometry. Similar primary fragmentation pathways involving partial loss of the ammonium cation were observed for species containing both one and two ammonium cations largely independent of the size, composition and charge state of the precursor ion. The [(C4H9)4N+] was found to exhibit stronger interactions with the core of the POMs resulting in higher abundance of fragment ions containing (C4H9) units compared to (C2H5) units originating from [(C2H5)4N+]. These results provide fundamental insight into the interactions between anionic metal oxides, heteroanions and ammonium cations that are responsible for the size and composition-controlled synthesis of POMs in solution.